Genetic Associations With Rapid Motor and Cognitive Deterioration in Parkinson’s Disease

Ling-Xiao Cao Beijing Tiantan Hospital Yingshan Piao Beijing Tiantan Hospital Yue Huang (  [email protected] ) Beijing Tiantan Hospital https://orcid.org/0000-0001-6051-2241

Research

Keywords: Parkinson's disease, susceptibility genes, single nucleotide polymorphisms, motor progression, rapid cognitive decline

Posted Date: March 1st, 2021

DOI: https://doi.org/10.21203/rs.3.rs-245594/v1

License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License

Page 1/18 Abstract

Background: Parkinson’s disease (PD) is caused by the interplay of genetic and environmental factors during brain aging. About 90 single nucleotide polymorphisms (SNPs) have been recently discovered associating with PD, but their associations with PD clinical features have not been fully characterized yet.

Methods: Clinical data of 377 patients with PD who enrolled in Parkinson's Progression Markers Initiative (PPMI) study were obtained. Patients with rapid cognitive or motor progression were determined through clinical assessments over fve years follow-up. In addition, genetic information of 50 targeted SNPs was extracted from the genetic database of NeuroX for the same cohort. Genetic associations with rapid motor and cognitive dysfunction of PD were analyzed using SPSS-logistic regression.

Results: Among 377 patients with PD, there are more male (31%) than female (17%) prone to have rapid motor progression (p<0.01), who demonstrate 16 points increase in the motor part assessment of MDS- UPDRS. There is no gender difference in rapid cognitive deterioration. Four SNPs (rs11724635, rs12528068, rs591323, rs17649553) were associated with fast cognitive decline (p<0.05) and the extended 50 SNPs researches excellent predicative value of area under curve (AUC) at 0.961. Three SNPs (rs823118, rs10797576, rs12456492) were associated with faster motor progression (p<0.05), and the extended 50 SNPs and gender researches fair prediction of AUC at 0.736. There were multiple genetic associations with initial clinical presentations of PD at baseline as well.

Conclusions: Genetic factors contribute to the disease progression as well as the clinical features at the disease onset.

Background

Parkinson disease (PD) is the second most common neurodegenerative disorder in the elderly, which is characterized by motor disabilities such as tremor, bradykinesia, rigidity as well as non-motor symptoms including hyposmia, REM sleep behavior disorder (RBD), cognitive impairment and so on[1, 2]. Both motor and non-motor disabilities are signifcant to patients’ quality of life and increase fnancial burden to the families and the society[3]. In addition to various combination of motor and non-motor presentations, the disease progression of each patient varies quite differently[4]. The rate of motor progression is the major factor related to prognosis and quality of life[5, 6]. Among non-motor symptoms, cognitive impairment and dementia are frequent problem encountered in PD especially at advanced stages of PD[1, 7]. At least 75% patients with PD who survive for more than 10 years will develop dementia[8]. Despite the high prevalence, our understanding of related mechanism is still limited. Therefore, identifying factors affecting the progression of motor and cognitive impairment of PD is particularly important for the discovery of PD pathogenesis, disease therapy and patient’s care.

Genetic contributions to PD and its susceptibility to the onset of PD have been well acknowledged[2, 9-11]. Meta-analysis of genome-wide association studies (GWAS) in 2017 and 2019 have successfully

Page 2/18 identifed more than 40 independent single nucleotide polymorphisms (SNPs) and 90 SNPs associated with PD[12, 13]. These 90 variants explained 16–36% of the heritable risk of PD depending on prevalence[13]. Recent studies showed that patients carrying a certain gene mutation have distinct clinical presentations and disease progression from sporadic PD[14, 15]. In addition, PD susceptibility genes have been associated with PD clinical features, such as the age of onset, progression of other non-motor symptoms of PD [16-21]. However, these studies were either based on cross-sectional PD cohorts or with limited genetic variants involved, so as to made incremental advances to the feld. Although recent genome-wide association study (GWAS) revealed genetic contributions to PD motor and cognitive progression in longitudinal PD cohorts[22], the clinical classifcation applied in that study might conceal signifcant genetic fndings. This study aims to investigate genetic associations with rapid motor and cognitive decline in a longitudinal PD cohort based on recent GWAS identifed PD risk SNPs[12, 13] .

Methods

Participants

Parkinson's Progression Markers Initiative (PPMI) is an observational international, multi-centre cohort study using advanced imaging, biologic sampling and clinical and behavioral assessments to identify biomarkers of PD progression, funded by Michael J. Fox Foundation (MJFF)[23]. Application to data usage was approved by the scientifc committee of PPMI, and this study involved database usage was approved by the Ethics Board of the Beijing Tiantan Hospital, Capital Medical University of China (KY 2018-031-02). A total 377 patients with clinical diagnosis of PD were selected in this study. All patients had been clinically assessed by Unifed Parkinson’s Disease Rating Scale (UPDRS), including UPDRS-III for motor function, Montreal Cognitive Assessment (MoCA) for cognitive function, and Rapid Eye Movement Behaviour Disorder Questionnaire (RBDQ), the University of Pennsylvania Smell Identifcation test (UPSIT), Scales for Outcomes in Parkinson’s disease - Autonomic (SCOPA-AUT), and Geriatric Depression Scale (GDS) for RBD, hyposmia, autonomic dysfunction, and depression respectively at baseline and annual examination basis up to fve years.

Baseline Evaluations

As studies suggested, cutoff values of 26, 5, 9, 5 were chosen for MoCA, RBDQ, SCOPA-AUT and GDS for the presence of the problems in cognition, RBD, autonomic dysfunction and depression [24-26]. Age at onset less than 55 years old was chosen as the cut-off value for early onset of PD[27].

Five-Year Follow-Up Evaluation

Determine PD Subgroup with Rapid Motor Progression: UPDRS is currently the most authoritative scale for evaluating PD motor symptoms. A number of studies have shown that the progression of motor symptoms is a non-linear pattern in the course of the disease[28]. Thus, we selected analyzing phase change in UPDRS-III score to defne motor progression. 3.2-point (95% CI 2.8 to 3.6) change per year in

Page 3/18 UPDRS-III score represents a rapid motor progression [29]. Thus, we identifed fast motor progressors if they had more than 16-point increase in the UPDRS-III score from baseline to the follow-up at year 5, and 99 patients (26%) were defned as fast motor progressors.

Determine PD Subgroup with Rapid Cognitive Dysfunction:

MoCA is a sensitive and widely used tool for cognitive function measurement in PD. Research showed that a four-point decrease in MoCA score is reliable to defne cognitive decline with 90% confdence [30]. Thus, from baseline to the follow-up year 5, we recognized 21 patients (5.6%) with fast cognitive decline meet with the defnitive standard ie. having more than four-point decrease in MoCA.

Genotyping and Selection of SNPs

Samples from PPMI were genotyped using NeuroX array. The NeuroX array is an Illumina Infnium iSelect HD Custom Genotyping array containing 267,607 Illumina standard contains exonic variants and an additional 24,706 custom variants designed for neurological disease studies. Out of the variants, approximately 12,000 are designed to study PD and are applicable to both large population studies of risk factors and investigations of familial disease with known mutations[31, 32]. All samples and genotypes underwent stringent quality controls (QC). Genetic data were cleaned using PLINK v1.9 beta. SNPs with missing genotype rate over 10%, minor allele frequency less than 0.02, and Hardy-Weinberg equilibrium (HWE) test p value less than 1×10-6 were excluded. Eventually 50 SNPs information were extracted as no further GWAS PD signifcant (p ≤ 5x10-8) were found in NeuroX or excluded by fltering (Supplementary Table 1).

Statistical Analysis

IBM SPSS Statistics 26 was used for this study. To assess genetic associations with rapid motor or cognitive decline, logistic regression was used to estimate odds ratios (OR) with 95% CI, p-values of each genetic variable, and the predictive values of total 50 SNPs with each phenotype were calculated. Receiver operating curve (ROC) analysis was used to assess the signifcant and total 50 SNPs for predicating the rapid cognitive and motor deterioration, and area under curves (AUC) were used to evaluate the predictive models. For the genetic association studies based on the initial clinical data collection, binary logistic regression was used for presence or absence of non-motor symptoms analysis with disease duration as a covariant as well, and linear regression was used for the onset age analysis.

Bioinformatics Analysis

STRING (version 11) website-based software was used to detect protein-protein interaction networks in supporting functional discovery in this polygenetic association datasets to generate common molecular pathways among different genetic products[33].

Results

Page 4/18 Clinical Observations

Baseline data observation: Of the 377 patients from PPMI database, 249 were men (66.0%) and the ratio of male vs female was 1.95. The median age at diagnosis was 61 years, 351 patients (93.1%) had hyposmia, detected by UPSIT test. As for other non-motor tests, median scores of SCOPA-AUT, GDS (Short version), RBDQ were 12, 5, and 4, respectively (Table 1). There were no signifcant gender differences in age of onset, progression of cognitive impairment, RBD symptoms, hyposmia symptoms, autonomic dysfunction, and depressive symptoms of this PD cohort (p>0.05).

Longitudinal observation: The median UPDRS-III motor score change was 8 by the ffth year follow up in this cohort. 99 (26%) patients had fast motor progression with median UPDRS-III motor score change of 22 by the 12th visit at the 5th year. 21 patients (5.6% of the cohort) had fast cognitive decline with median MoCA change of 5. there are more male (31%) than female (17%) prone to have rapid motor progression (p<0.01), but there is no gender difference in cognitive deterioration (Table 1).

Genetic Associations

Genetic associations with longitudinaldisease progression: Four SNPs (rs11724635, rs12528068, rs591323, rs17649553 located in the loci of BST1, RIMS1, FGF20, and MAPT respectively) associated with fast cognitive decline (p=0.025, p=0.008, p=0.019, p=0.024, respectively). Three SNPs (rs823118, rs10797576, rs12456492 located in the loci of NUCKS1, SIA1L2, RIT2 respectively) were associated with faster motor progression (p=0.028, p=0.039, p=0.018, respectively) (Table 2).

Genetic associations with clinical features at the baseline: Three SNPs (ITPKB rs4653767, FGF20 rs591323, GALC rs8005172) were associated with early onset age of PD (p=0.042, p=0.014, p=0.020, respectively); IP6K2 rs12497850 and LRRK2 rs76904798 were associated with cognitive impairment (p=0.006, p=0.007, respectively); SCN2A rs353116 was associated with hyposmia (p=0.002); NDUFAF2 rs2694528 and USP25 rs2823357 were associated with RBD (p=0.021, p=0.006, respectively), SATB1 rs4073221 and GAK rs11248051 were associated with autonomic dysfunction (p=0.034, p=0.043, respectively), and FGF20 rs591323 was associated with depression (p=0.034) (Supplementary Table 2).

ROC curve analysis

ROC curve analysis was performed to evaluate the predictive values of all and signifcant different SNPs for the outcomes of rapid motor and cognitive dysfunction (Figure 1). AUC of fast cognitive decline is 0.772 (95% CI 0.726 to 0.813) predicted by the signifcantly related SNPs (rs11724635, rs12528068, rs591323, rs17649553) (Table 2), while it reaches 0.961 (95% CI 0.937 to 0.978) with all 50 SNPs information input (Figure 1). The AUC of rapid motor progression is 0.628 predicted by the signifcantly related SNPs (rs823118, rs10797576, rs12456492) (Table 2), and it reaches 0.736 (95% CI 0.684 to 0.776) while considering all 50 SNPs and gender.

Page 5/18 Genetic factors also demonstrated fair predication properties (AUC=0.7-0.8) early onset age (0.744) and cognitive impairment (0.729) performances at baseline visit (Supplementary fgure 1). In addition, genetic factors also associate with other quantitative traits of PD at the initial visit, such as hyposmia (0.851), RBD (0.719), autonomic dysfunction (0.711), and depression (0.756) (supplementary fgure 2). p value of each ROC curve is less than 0.001.

Analysis of molecular pathways related to rapid motor and cognitive decline

STRING analysis showed the number of edges was 77 vs the expected of 11, average node degree was 3.28, and there was signifcant more interactions in this protein network (p< 1.0e-16). There were no direct interactive molecular pathways related to those gene products (BST1, RIMS1, FGF20 and tau) with signifcant implication for rapid cognitive decline, indicating they are independent risk factors. However, MAPT and FGF20 encode hub proteins with more than 5 molecular interactions (Figure 2)[34].

Regarding to the genes related to rapid motor progression, NUCKS1, SIPA1L2 and RIT2, NUCKS1 is an independent risk factor, and SIPA1L2 and RIT2 may jointly activate the RAS type GTPase. In addition, NUCKS1 and RIT2 are hub nodes in the network (Figure 2).

Discussion

Our study revealed up to 50 SNPs located in different genetic loci associated with the rapid cognitive and motor deterioration in PD (Table 2). Furthermore, we confrmed the predictive effect of susceptibility genes on rapid disease progression phenotypes through AUC analysis (Figure 1). In addition, we verifed the correlations between susceptibility genes and clinical quantitative traits in previous studies[35, 36] from genetic associations with clinical baseline data (Supplementary table and fgure).

In this study, we found there was more male with PD than female (Table 1). Gender was signifcantly related to rapid motor progression, but not related to other clinical features (Table 1). Previous study showed that female patients were more likely to have slower disease progression, due to higher dopaminergic activity at baseline and protective effect of estrogens[37]. Our results showed multi genetic network provide better predicative values for the measures of clinical features in PD (table 2, fgures 2, supplementary fgures 1 & 2). This partially explained why almost every patient with PD has non-motor symptoms ranging from 8 to 12 different symptoms, which is now considered as a crucial factor for driving quality of life of patients in PD[38]. FGF20 is the common gene showing signifcant association with multiple PD clinical features, early onset, depression and rapid cognitive decline (Table 2 & Supplementary Table 2). FGF20 rs591323 was associated with late onset age and rapid cognitive decline (see below), while older age at onset has been associated with a higher risk of dementia [39]. FGF20 is a hub protein interaction with SNCA, LRRK2, ACMSD, GAK, MCCC1 and GPNMB (Figure 2). Our study revealed the underlying molecular mechanisms and the molecular network as a whole contributing to the concurrent clinical features of PD.

Page 6/18 In this study, we found three variants NUCKS1 rs823118, SIPA1L2 rs10797576, RIT2 rs12456492 were associated with rapid motor deterioration in PD (Table 2). NUCKS1 is a hub protein with connection of TMEM175, MCCC1, ACMSD, LRRK2, GAK and FAM47E, and RIT2 is another hub node connecting with GAK, ACMSD, MCCC1, LRRK2, SNCA, MAPT and SIPA1L2 (Figure.2), while GBA and SNCA genes have been shown associated with rapid motor progression[21, 40-42]. Motor deterioration has been related to dopaminergic neuronal loss in the substantia nigra[43]. Microglial activation and neuroinfammation has been attributed to the neuronal cell death after the disease onset[44], while RIT2 enables to induce infammatory response[45]. In addition, impaired lysosomes, autophagosomes and mitochondria function in dopaminergic neurons facilitate α-synuclein deposits and subsequent neuronal death [46, 47], while TMEM175 and Lrrk2 have been attributed to this mechanism of PD. As 50 SNPs and gender together gave rise to a fair predication of rapid motor progression (Figure 1A), additional genetic factors are required to be identifed to achieve the most optimized predicative value for rapid motor progression.

Furthermore, our study identifed excellent genetic predicative markers for fast cognitive decline in PD (AUC=0.961, Figure 1B) under the foundation of rs11724635(in BST1 loci), rs12528068 (in RIMS1 loci), rs591323(in FGF20 loci), and rs17649553(in MAPT loci). Although all variants examined in this study are PD susceptible, both RIMS1 rs12528068 and MAPT rs17649553 demonstrated cognition protective effects (Table 2). Our fndings are consistent with the genetics - neuropathology association study[48], indicating the same genetic products may play different directions at the disease onset and during the disease progression. Indeed, based on the clinical data at the initial visit, when motor symptoms occur and onset of PD is often made, cognitive performance is associated with IP6K2 rs12497850 and LRRK2 rs76904798 in this cohort (Supplementary table 2), possibly through joint effects via their direct interaction (Figure 2). In this study, the most signifcant genetic impact on rapid cognitive decline is RIMS1 rs12528068 (p=0.008) (Table 2). Research showed that the T allele of rs12528068 increased the RIMS1 expression in the hippocampus[49], while RIMS1 is essential for maintaining normal probability of neurotransmitter release and has been shown involving in cognition processes in human[50].

This study has the following limitations. First, we focus on the main concerns of rapidity of motor and cognitive decline, rather than the disease progression profle, which incorporate other non-motor symptoms, such as pain, anxiety, fatigue and so on, due to limitation of database. Second, the NeuroX genetic data did not include all 90 SNPs recently summarized[13]. Consequently, we could not assess the associations between missing SNPs and symptoms of PD, which might lead to not ideal AUC value for predication of rapid motor progression. Third, patients enrolled in this study were mostly at early stage of PD, and some genetic variants may affect the disease progression at later stages, which were unable to be discovered in this study. Fourth, to our knowledge, this is the second paper reporting genetic associations with the progression of PD. Compared to the frst study from Tan MMX et al[22], our genetic variants coverage is not whole genome wide.

Conclusions

Page 7/18 Our study showed genetic factors not only contribute to the initial clinical presentations of PD, but also contribute to the rapidity of motor and cognitive deterioration of PD. The molecular pathways & network for fast cognitive decline in PD identifed in this study warrant validation in another cohort of PD.

Abbreviations

BST1, bone marrow stromal cell antigen 1;

FGF20, fbroblast growth factor 20;

GALC, galactosylceramidase;

GAK, cyclin G associated kinase;

IP6K2, inositol hexakisphosphate kinase 2;

ITPKB, inositol-trisphosphate 3-kinase B;

LRRK2, leucine rich repeat kinase 2;

MAPT, microtubule associated protein tau;

NDUFAF2, nicotinamide adenine dinucleotide ubiquinone oxidoreductase complex assembly factor 2;

NUCKS1, nuclear casein kinase and cyclin dependent kinase substrate 1;

RIMS1, regulating synaptic membrane exocytosis protein 1;

RIT2, ras like without CAAX motif 2;

SATB1, special AT-rich sequence-binding protein 1;

SCN2A, sodium voltage-gated channel alpha subunit 2;

SIPA1L2, signal induced proliferation associated 1 like 2;

USP25, ubiquitin specifc peptidase 25

Declarations

Ethics approval and consent to participate

The PPMI study was approved by the Institutional Review Boards of each PPMIsite. Informed written consent was obtained from all subjects at each site. Application to data usage was approved by the scientifc committee of PPMI, and this study involved database usage was approved by the Ethics Board of the Beijing Tiantan Hospital, Capital Medical University of China (KY 2018-031-02).

Page 8/18 Consent to publication

Not applicable.

Availability of data and material

The dataset information belongs to PPMI. The data analysis fles for this study are available from the corresponding author upon reasonable request.

Competing Interests

All authors consent for publication and have no competing interests.

Funding

The study was funded by National Natural Science Foundation of China (NSFC, 82071417).

Authors’ contributions

CLX did data extraction from the PPMI database, statistics analysis and drafted the manuscript. YSP revised the manuscript. YH designed the project and critically revised the manuscript.

Acknowledgements

Data used in the preparation of this article were obtained from the Parkinson’s Progression Markers Initiative (PPMI) database (www.ppmi-info.org/data). For up-to-date information on the study, visit www.ppmi-info.org. PPMI - a public-private partnership - is funded by the Michael J. Fox Foundation for Parkinson’s Research and funding partners, including Abbvie, Allergan, Amathus Therapeutics, Avid Radiopharmaceuticals, Biogen, Biolegend, Bristol-Myers Squibb, Celgene, Covance, GE Healthcare, Genentech, Golub Capital, Handl Therapeutics, Insitro, Janssen Neuroscience, Lilly, Lundbeck, Merck, Meso Scale Discovery, Neurocrine, Pfzer, Piramal, Prevail Therapeutics, Roche, Sanof Genzyme, Servier, Takeda, Teva, Ucb, Verily and Voyager Therapeutics.

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Tables

Table 1. Demographic and Clinical Characteristics of the PD Cohort

Clinical Characteristics Median (IQR) P value* Male Female Total

Number of people, No./total No. (%) 249/377 128/377 377/377 <0.01 (66%) (34%) (100%)

Age at diagnosis, median (IQR) 62 (55 61 (54 61 (54 N.S. to 69) to 68) to 68)

Age at baseline examination, median (IQR) 63 (55 62 (55 62 (54 N.S. to 69) to 68) to 69)

Years of education, median (IQR) 16 (14 16 (13 16 (14 N.S. to 18) to 17) to 18)

UPDRS-III motor score change per 5 years, median (IQR) 9 (1 to 7 (0 to 8 (0 to N.S. 16) 13) 16)

Rapid motor progression (increasing scores ≥ 16 77/249 22/128 99/377 <0.01 points), No./total No. (%) (31%) (17%) (26%)

UPDRS-III motor score change per 5 years among fast 22 (17 22 (20 22 (18 N.S. motor progression patients, median (IQR) to 28) to 28) to 28)

MoCA cognition score at baseline, median (IQR) 27 (24 27 (25 27 (25 N.S. to 29) to 29) to 29)

MoCA change per 5 years, median (IQR) 0 (-1 to 0 (0 to 0 (-1 to N.S. 1) 0) 1)

Rapid cognitive decline (decrease in score ≥ 4 points), 14/249 7/128 21/377 N.S. No./total No. (%) (5.6%) (5.5%) (5.6%)

Scales for SCOPA-AUT, median (IQR) 12 (7 to 11(7 to 12 (7 to N.S. 17) 15) 16)

Geriatric Depression Scale (Short version), median 5 (5 to 5 (5 to 5 (5 to N.S. (IQR) 6) 6) 6)

Rapid Eye Movement Behaviour Disorder Questionnaire, 4 (2 to 4 (3 to 4 (3 to N.S. median (IQR) 8) 7) 7)

UPSIT, Hyposmia No./total No. (%) 235 116 351/377 N.S. (94%) (91%) (93%)

Page 14/18 Abbreviations: UPDRS-III, Unifed Parkinson’s Disease Rating Scale part III; MoCA, Montreal Cognitive Assessment; SCOPA-AUT, Scales for Outcomes in Parkinson’s disease -Autonomic; UPSIT, the University of Pennsylvania Smell Identifcation test; IQR interquartile range; N.S.=not signifcant; *Chi-Square test was used.

Table 2. Genetic Associations with Rapid Motor and Cognitive Deterioration in PD

Rapid Motor Progression

SNP Related Gene OR (95%CI) Beta P Value RR (95%CI)

rs823118 NUCKS1 1.46 (1.04-2.04) 0.38 0.028 1.12 (0.94-2.56)

rs10797576 SIPA1L2 0.59 (0.36-0.97) -0.53 0.039 0.86 (0.76-0.98)

rs12456492 RIT2 1.50 (1.07-2.10) 0.41 0.018 1.11 (0.98-1.25)

Fast Cognitive Decline

SNP Related Gene OR (95%CI) Beta P Value RR (95%CI)

rs11724635 BST1 2.07 (1.10-3.90) 0.73 0.025 1.04 (0.99-1.09)

rs12528068 RIMS1 0.27 (0.10-0.70) -1.33 0.008 0.70 (0.17-2.86)

rs591323 FGF20 2.35 (1.15-4.80) 0.85 0.019 1.03 (0.98-1.09)

rs17649553 MAPT 0.24 (0.07-0.83) -1.43 0.024 0.93 (0.89-0.97)

Abbreviations: SNP, single nucleotide polymorphism; OR, odds ratio; RR, relative risk.

Figures

Page 15/18 Figure 1

ROC Curve Analysis Showing Genetic Prediction of Rapid Motor and Cognitive Deterioration in PD. A. Strategic SNPs give rise to 0.628 AUC, while 50 SNPs together reach fair predication of rapid motor progression (AUC=0.731). When considering gender, strategic SNPs and 50 SNPs respectively reach a higher AUC level (AUC=0.631, AUC=0.736). B. Strategic SNPs give rise to 0.772 AUC, while 50 SNPs together reach excellent predication of fast cognitive decline (AUC=0.961); Abbreviations: ROC, receiver operating characteristic curve; AUC, area under curve; SNP, single nucleotide polymorphism; Strategic SNPs for rapid progression of motor and cognitive dysfunction, seeing Table 2.

Page 16/18 Figure 2

Molecular Interactions of PD Related Genes Involved in This Study. A total 47 protein coding genes were input into the STRING analysis. The black color highlighted are the genes related to fast cognitive decline, and the red color highlighted are the genes related to rapid motor progression. Black lines represent protein-protein interactions, and thicker lines represent stronger links.

Supplementary Files

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SupplementaryTable.docx Suppl.Fig.1.tif

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